def hierarchy(self, hierarchy):
"""Define the ConKit :obj:`~conkit.core.sequencefile.SequenceFile` """
if hierarchy and _isinstance(hierarchy, "SequenceFile") and hierarchy.is_alignment:
self._hierarchy = hierarchy
elif hierarchy and _isinstance(hierarchy, "SequenceFile"):
raise TypeError("Provided hierarchy does not show characteristics of an alignment")
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
def _parse_dssp(self, dssp):
"""Parse :obj:`Bio.PDB.DSSP.DSSP` into a :obj:`pandas.DataFrame` with secondary structure information
about the model"""
if not tools._isinstance(dssp, DSSP):
raise TypeError("Invalid hierarchy type for dssp: %s" %
dssp.__class__.__name__)
_dssp_list = []
for residue in sorted(dssp.keys(), key=lambda x: x[1][1]):
resnum = residue[1][1]
if resnum in self.absent_residues:
_dssp_list.append((resnum, np.nan, np.nan, np.nan, np.nan))
continue
acc = dssp[residue][3]
if dssp[residue][2] in ('-', 'T', 'S'):
ss2 = (1, 0, 0)
elif dssp[residue][2] in ('H', 'G', 'I'):
ss2 = (0, 1, 0)
else:
ss2 = (0, 0, 1)
_dssp_list.append((resnum, *ss2, acc))
dssp = pd.DataFrame(_dssp_list)
dssp.columns = ['RESNUM', 'COIL', 'HELIX', 'SHEET', 'ACC']
return dssp
def hierarchy(self, hierarchy):
"""Define the default contact map hierarchy"""
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._hierarchy = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" %
hierarchy.__class__.__name__)
def hierarchy(self, hierarchy):
"""Define the ConKit :obj:`ContactMap <conkit.core.contactmap.ContactMap>`
Raises
------
TypeError
The hierarchy is not an contact map
"""
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._hierarchy = hierarchy
else:
raise TypeError("The hierarchy is not an contact map")
def hierarchy(self, hierarchy):
"""Define the ConKit :obj:`~conkit.core.contactmap.ContactMap`
Raises
------
:exc:`RuntimeError`
The hierarchy is not an alignment
"""
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._hierarchy = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
def hierarchy(self, hierarchy):
if hierarchy and _isinstance(hierarchy, "Distogram"):
self._hierarchy = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" %
hierarchy.__class__.__name__)
def test__isinstance_4(self):
h = Sequence("test", "AAAA")
self.assertTrue(tools._isinstance(h, "Sequence"))
def test__isinstance_5(self):
h = SequenceFile("test")
self.assertTrue(tools._isinstance(h, "SequenceFile"))
def test__isinstance_2(self):
h = ContactMap("test")
self.assertTrue(tools._isinstance(h, "ContactMap"))
def test__isinstance_3(self):
h = ContactFile("test")
self.assertTrue(tools._isinstance(h, "ContactFile"))
def other(self, hierarchy):
if hierarchy and _isinstance(hierarchy, "ContactMap"):
self._other = hierarchy
else:
raise TypeError("Invalid hierarchy type: %s" % hierarchy.__class__.__name__)
def test__isinstance_1(self):
h = Contact(1, 2, 2)
self.assertTrue(tools._isinstance(h, "Contact"))
def test__isinstance_7(self):
self.assertFalse(tools._isinstance(5, str))
def test__isinstance_6(self):
self.assertTrue(tools._isinstance(5, int))
def sequence(self, sequence):
if sequence and tools._isinstance(sequence, "Sequence"):
self._sequence = sequence
else:
raise TypeError("Invalid hierarchy type for sequence: %s" %
sequence.__class__.__name__)
def prediction(self, prediction):
if prediction and tools._isinstance(prediction, "Distogram"):
self._prediction = prediction
else:
raise TypeError("Invalid hierarchy type for prediction: %s" %
prediction.__class__.__name__)
def model(self, model):
if model and tools._isinstance(model, "Distogram"):
self._model = model
else:
raise TypeError("Invalid hierarchy type for model: %s" %
model.__class__.__name__)
